Zfp423 binds autoregulatory sites in p19 cell culture model

TY - JOUR

T1 - Zfp423 binds autoregulatory sites in p19 cell culture model

AU - Cho, Young-Wook

AU - Hong, Chen-Jei

AU - Hou, Aiju

AU - Gent, Peter M

AU - Zhang, Kuixing

AU - Won, Kyoung-Jae

AU - Hamilton, Bruce A

PY - 2013/6/6

Y1 - 2013/6/6

N2 - Zfp423 is a 30 zinc finger transcription factor that forms regulatory complexes with EBF family members and factors targeted by canonical signaling pathways. Zfp423 mutations produce a range of developmental abnormalities in mice and humans related to the ciliopathies. Surprisingly, computational analysis of clustered Zfp423 and partner motifs in conserved genomic sequences predicts enrichment in Zfp423 and Ebf genes. In cell culture models selected for Zfp423 and EBF expression, we identify strong and reproducible occupancy of two Zfp423 intronic sites using chromatin immunoprecipitation with multiple independent antibodies. Both sites are significantly enriched in either quantitative PCR or massively parallel sequencing assays. A site in intron 5 acts as a classical enhancer in transient assays, but does not require the consensus motif for activity, suggesting a redundant or modulatory role for Zfp423 binding in this context. We speculate that Zfp423 may repress this enhancer as part of a developmental ratchet.

AB - Zfp423 is a 30 zinc finger transcription factor that forms regulatory complexes with EBF family members and factors targeted by canonical signaling pathways. Zfp423 mutations produce a range of developmental abnormalities in mice and humans related to the ciliopathies. Surprisingly, computational analysis of clustered Zfp423 and partner motifs in conserved genomic sequences predicts enrichment in Zfp423 and Ebf genes. In cell culture models selected for Zfp423 and EBF expression, we identify strong and reproducible occupancy of two Zfp423 intronic sites using chromatin immunoprecipitation with multiple independent antibodies. Both sites are significantly enriched in either quantitative PCR or massively parallel sequencing assays. A site in intron 5 acts as a classical enhancer in transient assays, but does not require the consensus motif for activity, suggesting a redundant or modulatory role for Zfp423 binding in this context. We speculate that Zfp423 may repress this enhancer as part of a developmental ratchet.

KW - Animals

KW - Binding Sites

KW - Cell Line, Tumor

KW - Chromatin Immunoprecipitation

KW - DNA-Binding Proteins/genetics

KW - Enhancer Elements, Genetic

KW - Gene Expression Regulation, Developmental

KW - Genes, Reporter

KW - Humans

KW - Introns

KW - Luciferases/metabolism

KW - Mice

KW - Models, Biological

KW - Molecular Sequence Data

KW - Mutation

KW - Protein Binding

KW - Protein Isoforms/genetics

KW - Sequence Analysis, DNA

KW - Signal Transduction

KW - Transcription Factors/genetics

U2 - 10.1371/journal.pone.0066514

DO - 10.1371/journal.pone.0066514

M3 - Journal article

C2 - 23762491

SN - 1932-6203

VL - 8

SP - e66514

JO - PLOS ONE

JF - PLOS ONE

IS - 6

ER -